Are your wires as short as possible and of equal length? Are they twisted up or separated. Try sticking a sheet of card board between the two rows to help keep them apart.
This is the same issue I had when I used ribbon cable.
If all else fails take a sheet of foil and fold it into 3 layers. Cut it to fit in between the two rows. Solder a wire onto it and connect it to ground. Cover the foil with packaging tape and use it to separate the two rows. In effect you are creating a cheap RF shield. Don't know if it will work but you can try.
Oh and I want to see some pictures!!
edit// measure the 5V lines on the cart slot on the 32x side and make sure it isn't fluctuating.